|
Status |
Public on Jan 04, 2020 |
Title |
Replicate1_T14 |
Sample type |
SRA |
|
|
Source name |
Capsaspora adherent cells_11h45 after release
|
Organism |
Capsaspora owczarzaki |
Characteristics |
cell type: Filopodial strain: ATCC 30864 treatment: Released from cell cycle overnight arrest using Hydroxyurea 10mM time point: 11h45 after release
|
Treatment protocol |
Cultures at 30-50% confluency were treated with Hydroxyurea to a final concentration of 10mM, and left incubating for 14 hours overnight. Cells were released from Hydroxyurea by washing prior to elution in fresh medium; samples were collected by scraping and washing two hours after release, and from there on every 45 minutes until thirteen hours.
|
Growth protocol |
Cells were incubated at 23 degrees Celsius in ATCC medium 1034 (modified PYNFH medium).
|
Extracted molecule |
total RNA |
Extraction protocol |
Time point samples were washed in 1xPBS, poured in Trizol, and frozen at -80oC. Total RNA was purified using Zymo RNA miniprep kit (Zymo Research, Irvine, CA, USA, #R2050). mRNA libraries were prepared using the TruSeq Stranded mRNA Sample Prep kit
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
t14_23785_ATGTCA_L007 processed data file: R1_table_tpms.txt
|
Data processing |
Transcriptome mapping for every independent time point using kallisto v0.43.1 with standard parameters (-q read1 read2) onto a set of the largest isoforms of the Capsaspora transcriptome. Genome_build: Capsaspora genome v3 (Iñaki Ruiz-Trillo lab) https://figshare.com/articles/Genome_-_Capsaspora_owczarzaki_v3_/4123158/2 Supplementary_files_format_and_content: Resulting transcript-per-million lists from kallisto of every sample bound together in columns of a single matrix using bash and awk
|
|
|
Submission date |
Nov 28, 2019 |
Last update date |
Jan 04, 2020 |
Contact name |
Alberto Perez-Posada |
E-mail(s) |
alberto.perez@upf.edu
|
Organization name |
Institut de Biologia Evolutiva
|
Lab |
Multicellgenome Lab
|
Street address |
Passeig Marítim de la Barceloneta, 37-49
|
City |
Barcelona |
ZIP/Postal code |
08003 |
Country |
Spain |
|
|
Platform ID |
GPL27855 |
Series (1) |
GSE141156 |
Gradual evolution of cell cycle regulation by cyclin-dependant kinases during the transition to animal multicellularity |
|
Relations |
BioSample |
SAMN13423093 |
SRA |
SRX7237419 |